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There are, of course, many ways such a thing could be accomplished. The simplest way I can think of at the moment, would be to utilize a future feature. We are already planning to implement some variation of user defined 'bookmarks' in genomic space. These would be organizable to some extent and exportable in one or more formats which may be useful elsewhere. Once that feature has been implemented, we could conceivably write a script for SVS to read the exported 'bookmark' list (your flagged variant list, in this case) and mask all intersections in one or more spreadsheets of your choosing.
In short, your procedure would be:
